Improving protein fold recognition using triplet network and ensemble deep learning. - Yan Liu 038; Ke Han; Yi-Heng Zhu 001; Ying Zhang 053; Long-Chen Shen; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2021)

SAResNet: self-attention residual network for predicting DNA-protein binding. - Long-Chen Shen; Yan Liu 038; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2021)

MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. - Ke Han; Long-Chen Shen; Yi-Heng Zhu 001; Jian Xu 009; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2022)

Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. - Yan Liu 038; He Yan; Long-Chen Shen; Dong-Jun Yu (J. Chem. Inf. Model., 2023)

TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level. - Yan Liu 038; Guo Wei; Chen Li 021; Long-Chen Shen; Robin B. Gasser; Jiangning Song; Dijun Chen; Dong-Jun Yu (Briefings Bioinform., 2023)

Integrating unsupervised language model with multi-view multiple sequence alignments for high-accuracy inter-chain contact prediction. - Zi Liu; Yi-Heng Zhu 001; Long-Chen Shen; Xuan Xiao; Wangren Qiu; Dong-Jun Yu (Comput. Biol. Medicine, 2023)

GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. - Shuo Li; Yan Liu 038; Long-Chen Shen; He Yan; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2024)

scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data. - Yan Liu 038; Chen Li 021; Long-Chen Shen; He Yan; Guo Wei; Robin B. Gasser; Xiaohua Hu 001; Jiangning Song; Dong-Jun Yu (Comput. Biol. Medicine, 2025)

Supervised contrastive learning enhances MHC-II peptide binding affinity prediction. - Long-Chen Shen; Yan Liu 038; Zi Liu; Yumeng Zhang; Zhikang Wang; Yuming Guo 001; Jamie Rossjohn; Jiangning Song; Dong-Jun Yu (Expert Syst. Appl., 2025)